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Yorodumi- PDB-4gq0: Crystal structure of AKR1B10 complexed with NADP+ and Caffeic aci... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4gq0 | |||||||||
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Title | Crystal structure of AKR1B10 complexed with NADP+ and Caffeic acid phenethyl ester | |||||||||
Components | Aldo-keto reductase family 1 member B10 | |||||||||
Keywords | OXIDOREDUCTASE / alpha-beta TIM barrel / NADP-dependant oxidoreductase / Caffeic acid phenethyl ester and NADP+ | |||||||||
Function / homology | Function and homology information indanol dehydrogenase activity / alcohol dehydrogenase (NADP+) activity / farnesol catabolic process / geranylgeranyl reductase activity / cellular detoxification of aldehyde / aldo-keto reductase (NADPH) activity / NADP-retinol dehydrogenase / allyl-alcohol dehydrogenase / allyl-alcohol dehydrogenase activity / all-trans-retinol dehydrogenase (NADP+) activity ...indanol dehydrogenase activity / alcohol dehydrogenase (NADP+) activity / farnesol catabolic process / geranylgeranyl reductase activity / cellular detoxification of aldehyde / aldo-keto reductase (NADPH) activity / NADP-retinol dehydrogenase / allyl-alcohol dehydrogenase / allyl-alcohol dehydrogenase activity / all-trans-retinol dehydrogenase (NADP+) activity / daunorubicin metabolic process / doxorubicin metabolic process / retinal dehydrogenase activity / aldose reductase (NADPH) activity / retinoid metabolic process / Retinoid metabolism and transport / lysosome / mitochondrion / extracellular region / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | |||||||||
Authors | Liping, Z. / Xuehua, Z. / Shangke, C. / Jing, Z. / Xiaopeng, H. | |||||||||
Citation | Journal: To be Published Title: Crystal structure of AKR1B10 complexed with NADP+ and Caffeic acid phenethyl ester Authors: Liping, Z. / Xuehua, Z. / Shangke, C. / Jing, Z. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4gq0.cif.gz | 84 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4gq0.ent.gz | 61.2 KB | Display | PDB format |
PDBx/mmJSON format | 4gq0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4gq0_validation.pdf.gz | 720.2 KB | Display | wwPDB validaton report |
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Full document | 4gq0_full_validation.pdf.gz | 720.5 KB | Display | |
Data in XML | 4gq0_validation.xml.gz | 15.3 KB | Display | |
Data in CIF | 4gq0_validation.cif.gz | 21.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gq/4gq0 ftp://data.pdbj.org/pub/pdb/validation_reports/gq/4gq0 | HTTPS FTP |
-Related structure data
Related structure data | 1zuaS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 36297.754 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Strain: Human / Gene: AKR1B10 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 References: UniProt: O60218, Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor |
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#2: Chemical | ChemComp-QAP / |
#3: Chemical | ChemComp-NAP / |
#4: Water | ChemComp-HOH / |
Sequence details | THIS RESIDUE CORRESPOND |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.56 Å3/Da / Density % sol: 51.91 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 9 Details: 100mM Tris, 30-35% PEG6000, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SEALED TUBE / Type: OXFORD DIFFRACTION ENHANCE ULTRA / Wavelength: 1.5418 Å |
Detector | Type: OXFORD ONYX CCD / Detector: CCD / Date: May 21, 2012 |
Radiation | Monochromator: multilayer optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→24.8 Å / Num. all: 21351 / Num. obs: 21323 / % possible obs: 99.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.2 % / Biso Wilson estimate: 27.5 Å2 / Rmerge(I) obs: 0.083 / Rsym value: 0.067 / Net I/σ(I): 16.8 |
Reflection shell | Resolution: 2.1→2.21 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.543 / Mean I/σ(I) obs: 3.2 / Num. unique all: 3033 / % possible all: 98.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1ZUA Resolution: 2.1→23.646 Å / Occupancy max: 1 / Occupancy min: 0.48 / FOM work R set: 0.8495 / SU ML: 0.27 / σ(F): 1.79 / Phase error: 22.49 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.788 Å2 / ksol: 0.327 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 80.75 Å2 / Biso mean: 28.7039 Å2 / Biso min: 7.4 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→23.646 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8
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